[ccp4bb] Intra-molecular interactions
Dear All: I have a quick question: how common it is that electrostatic interactions are involved in intra-molecular interactions, particularly in intrinsically disordered proteins? Is this interaction specific and any example? Thanks, Dee Xiaodi Yu, Ph.D. Boston Children's Hospital Dana-Farber Cancer Institute Harvard Medical School 3 Blackfan Boston, MA 02115
Re: [ccp4bb] Intra-molecular interactions
Dee, Intramolecular electrostatic interactions are common in protein structures, for example between i and i+4 pairs on the same face of a helix. Robert Baldwin (Stanford) and others did a lot of work on the contribution of intramolecular salt bridges to helix stabilization in model helices. If I remember correctly, some of his studies indicated that disrupting the ionic interaction could completely destabilize the helix. Your real question is if they play a role in disordered regions. The way I think about this is that an intramolecular salt bridge may be able to induce structure in an otherwise disordered region (if the pairs are strategically located). Alternatively, the entropic penally of folding may be too much to pay for by the enthalpy gain due to such an interaction (remember solvation). The bottom line is that the fact that it is disordered means the interaction is not contributing significantly. Chitta - Original Message - From: Xiaodi Yu uppsala@hotmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Saturday, November 3, 2012 12:06:32 PM Subject: [ccp4bb] Intra-molecular interactions Dear All: I have a quick question: how common it is that electrostatic interactions are involved in intra-molecular interactions, particularly in intrinsically disordered proteins? Is this interaction specific and any example? Thanks, Dee Xiaodi Yu, Ph.D. Boston Children's Hospital Dana-Farber Cancer Institute Harvard Medical School 3 Blackfan Boston, MA 02115
Re: [ccp4bb] Intra-molecular interactions
On 11/03/2012 12:06 PM, Xiaodi Yu wrote: how common it is that electrostatic interactions are involved in intra-molecular interactions, particularly in intrinsically disordered proteins? It's impossible to answer your question unless you define what you mean by degree of commonality. If you are asking if salt bridges happen - yes, they do. All the time. On the other hand, it must be impossible to conclude anything with certainty about details of interactions within intrinsically disordered proteins. It's impossible to determine their structure because they are, well, disordered. But I know of no law of physics that would prevent electrostatic interactions in such molecules. Cheers, Ed. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
Re: [ccp4bb] Intra-molecular interactions
For some starting points, google electrostatic interactions in intrinsically disordered proteins. Of course they occur in IDPs; they even have proportionally more charged residues than folded proteins. Petri On Nov 3, 2012, at 5:06 PM, Xiaodi Yu wrote: Dear All: I have a quick question: how common it is that electrostatic interactions are involved in intra-molecular interactions, particularly in intrinsically disordered proteins? Is this interaction specific and any example? Thanks, Dee Xiaodi Yu, Ph.D. Boston Children's Hospital Dana-Farber Cancer Institute Harvard Medical School 3 Blackfan Boston, MA 02115 --- Petri Kursula, PhD Group Leader, Docent of Neurobiochemistry Department of Biochemistry Biocenter Oulu, University of Oulu, Finland Department of Chemistry, University of Hamburg, Germany Visiting Scientist (CSSB-HZI, DESY, Hamburg, Germany) www.biochem.oulu.fi/kursula www.desy.de/~petri petri.kurs...@oulu.fi petri.kurs...@desy.de ---
